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- Creator:
- Thessen, Anne E., Bunkers, Daniel E., Buttigieg, Pier Luigi, Cooper, Laurel D., Dahdul, Wasila M., Domisch, Sami, Franz, Nico M., Jaiswal, Pankaj, Lawrence-Dill, Carolyn J., Midford, Peter E., Mungall, Christopher J., Ramírez, Martín J., Specht, Chelsea D., Vogt, Lars, Aldo Vos, Rutger, Walls, Ramona L., White, Jeffrey W., Zhang, Guanyang, Deans, Andrew R., Huala, Eva, Lewis, Suzanna E., and Mabee, Paula M.
- Abstract:
- Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
- Resource Type:
- Article
- Full Text:
- , P. L., Cooper, L. D., Dahdul, W. M., Domisch, S., ... & Mungall, C. J. (2015). Emerging semantics
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- Creator:
- Arighi, Cecilia N., Carterette, Ben, Cohen, K. Bretonnel, Krallinger, Martin, Wilbur, W. John, Fey, Petra, Dodson, Robert, Cooper, Laurel, Van Slyke, Ceri E., Dahdul, Wasila, Mabee, Paula, Li, Donghui, Harris, Bethany, Gillespie, Marc, Jimenez, Silvia, Roberts, Phoebe, Matthews, Lisa, Becker, Kevin, Drabkin, Harold, Bello, Susan, Licata, Luana, Chatr-aryamontri, Andrew, Schaeffer, Mary L., Park, Julie, Haendel, Melissa, Van Auken, Kimberly, Li, Yuling, Chan, Juancarlos, Muller, Hans-Michael, Cui, Hong, Balhoff, James P., Wu, Johnny Chi-Yang, Lu, Zhiyong, Wei, Chih-Hsuan, Tudor, Catalina O., Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar, Cejuela, Juan Miguel, Dubey, Pratibha, and Wu, Cathy
- Abstract:
- In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have...
- Resource Type:
- Article
- Full Text:
- . Van Slyke8, Wasila Dahdul9, Paula Mabee9, Donghui Li10, Bethany Harris5, Marc Gillespie11, Silvia
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- Creator:
- Deans, Andrew R., Lewis, Suzanna E., Huala, Eva, Anzaldo, Salvatore S., Ashburner, Michael, Balhoff, James P., Blackburn, David C., Blake, Judith A., Burleigh, J. Gordon, Chanet, Bruno, Cooper, Lauren D., Courtot, Mélanie, Csösz, Sándor, Cul, Hong, Dahdul, Wasila, Das, Sandip, Dececchi, T. Alexander, Dettal, Agnes, Diogo, Rui, Druzinsky, Robert E., Dumontier, Michel, Franz, Nico M., Friedrich, Frank, Gkoutos, George V., Haendel, Melissa, Harmon, Luke J., Hayamizu, Terry F., He, Yongqun, Hines, Heather M., Ibrahim, Nizar, Jackson, Laura M., Jaiswal, Pankaj, James-Zorn, Christina, Köhler, Sebastian, Lecointre, Guillaume, Lapp, Hilmar, Lawrence, Carolyn J., Le Novère, Nicolas, Lundberg, John G., Macklin, James, Mast, Austin R., Midford, Peter E., Mikó, István, Mungall, Christopher J., Oellrich, Anika, Osumi-Sutherland, David, Parkinson, Helen, Ramírez, Martín J., Richter, Stefan, Robinson, Peter N., Ruttenberg, Alan, Schulz, Katja S., Segerdell, Erik, Seltmann, Katja C., Sharkey, Michael J., Smith, Aaron D., Smith, Barry, Specht, Chelsea D., Squires, R. Burke, Thacker, Robert W., Thessen, Anne, Fernandez-Triana, Jose, Vihinen, Mauno, Vize, Peter D., Vogt, Lars, Wall, Christine E., Walls, Ramona L., Westerfeld, Monte, Wharton, Robert A., Wirkner, Christian S., Woolley, James B., Yoder, Matthew J., Zorn, Aaron M., and Mabee, Paula
- Abstract:
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
- Resource Type:
- Article
- Full Text:
- through Phenotypes Deans, A. R., Lewis, S. E., Huala, E., Anzaldo, S. S., Ashburner, M., et al. (2015
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- Creator:
- Walls, Ramona L., Athreya, Balaji, Cooper, Laurel, Elser, Justin, Gandolfo, Maria A., Jaiswal, Pankaj, Mungall, Christopher J., Preece, Justin, Rensing, Stefan, Smith, Barry, and Stevenson, Dennis W.
- Abstract:
- Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web....
- Resource Type:
- Article
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- Creator:
- Bogan, Sergio, Sidlauskas, Brian, Vari, Richard P., and Agnolin, Federico
- Abstract:
- The fossil species Arrhinolemur scalabrinii, which was described from late Miocene deposits of Entre Ríos, Argentina, is reevaluated. Whereas the species was originally placed in the Primates (Mammalia) and later made the unique member of the order Arrhinolemuroidea within the Mammalia, our analysis indicates that the specimen is rather a...
- Resource Type:
- Article
- Full Text:
- Partido de Merlo, Buenos Aires. Jornadas Paleontológicas del Centro, Olavarría, 16-17. Cione, A. L., M. M
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- Creator:
- Frable, Benjamin W.
- Abstract:
- Neotropical characiform fishes form one of the most diverse freshwater ichthyofauna in the world. Knowledge of evolutionary processes that generated and maintain the immense characiform lineage and morphological diversity is still poorly understood. When did characiform lineages diversify? How have major geological and environmental changes affected diversification? Why are some...
- Resource Type:
- Masters Thesis
- Full Text:
- !within! the!geophagine!cichlids!(LópezZFernández!et!al.,!2005).!Dahdul!(2010)!noted! morphological
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- Creator:
- Cooper, Laurel, Walls, Ramona L., Elser, Justin, Gandolfo, Maria A., Stevenson, Dennis W., Smith, Barry, Preece, Justin, Athreya, Balaji, Mungall, Christopher J., Rensing, Stefan, Hiss, Manuel, Lang, Daniel, Reski, Ralf, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Schaeffer, Mary, Menda, Naama, Arnaud, Elizabeth, Shrestha, Rosemary, Yamazaki, Yukiko, and Jaiswal, Pankaj
- Abstract:
- The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
- Resource Type:
- Article
- Full Text:
- been developed since then include the Teleost Anatomy Ontology (Dahdul et al. 2010), and Uberon, a
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- Creator:
- Oellrich, Anika, Walls, Ramona L., Cannon, Ethalinda K. S., Cannon, Steven B., Cooper, Laurel, Gardiner, Jack, Gkoutos, Georgios V., Harper, Lisa, He, Mingze, Hoehndorf, Robert, Jaiswal, Pankaj, Kalberer, Scott R., Lloyd, John P., Meinke, David, Menda, Naama, Moore, Laura, Nelson, Rex T., Pujar, Anuradha, Lawrence, Carolyn J., and Huala, Eva
- Abstract:
- BACKGROUND: Plant phenotype datasets include many different types of data, formats, and terms from specialized vocabularies. Because these datasets were designed for different audiences, they frequently contain language and details tailored to investigators with different research objectives and backgrounds. Although phenotype comparisons across datasets have long been possible on a...
- Resource Type:
- Article
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- Creator:
- Lyons, Donald E.
- Abstract:
- This dissertation focuses on the predator-prey relationship between two species of avian predators, Caspian terns (Hydroprogne caspia) and double-crested cormorants (Phalacrocorax auritus), and one of their important prey types, juvenile salmonids (Oncorhynchus spp.), in the Columbia River estuary of Oregon and Washington states during the period 1998 – 2007. I...
- Resource Type:
- Dissertation
- Full Text:
- River estuary, Oregon, U.S.A. Waterbirds 27: 155-160. 10 1 0 Antolos, M., Roby, D.D
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- Creator:
- Burns, Michael D.
- Abstract:
- Characiform fishes form one of the most diverse freshwater fish clades in the world. Comprising more than 2000 species and distributed primarily in South America and Africa, characiforms vary dramatically in their ecomorphology. However, the evolutionary processes responsible for the immense ecomorphological diversity remains unknown. Recently, a study postulated that...
- Resource Type:
- Dissertation